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Data for the LJ fluid properties: a pressure variation with density, and b viscosity variation with density. MD data points from pre-simulation (circles), fitted polynomial (solid lines) and NIST data (Linstrom and Mallard 2001) (dashed lines)
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We present a procedure for using molecular dynamics (MD) simulations to provide essential fluid and interface properties for subsequent use in computational fluid dynamics (CFD) calculations of nanoscale fluid flows. The MD pre-simulations enable us to obtain an equation of state, constitutive relations, and boundary conditions for any given fluid/...
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... Bulk pressure as a function of bulk density Figure 2a shows MD pre-simulation measurements of pressure, obtained from the standard Irving and Kirkwood expression (1950), varying with the mass density. ...
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... to a second-order polynomial. This then serves as an equation of state within the enhanced CFD solver to connect the mass continuity equation to the momentum equation. In this case, the polynomial is p ¼ 0:001559q 2 À 3:387q þ 2020:6. For reference, data from the NIST database for argon (Linstrom and Mallard 2001) are also plotted in Fig. 2a and is in close agreement with our MD pre-simulation data. Clearly, in this particular case, properties for argon are well known, but we extract the equation of state from our MD pre- simulation for the purposes of demonstration. The equation of state (and the viscosity equation in the following subsection) could be obtained by ...
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... the relaxed and time-averaged velocity profile. The applied shear stress is measured using the Irving-Kirkwood equation and then compared with the strain rate using Eq. (1) to give a dynamic shear viscosity coefficient for L-J argon at a given bulk density. The vis- cosity coefficients measured from our MD pre-simulations of LJ argon are shown in Fig. 2b. A least-squares poly- nomial fit of 2nd order in density is also plotted: l ¼ 7:96 Â 10 À10 q 2 À 1:774 Â 10 À6 q þ 0:001106. This is then used in our enhanced CFD simulations to close the momentum equation. Again, for reference, data from the NIST database for liquid argon are also plotted in Fig. 2b. Note, due to the breakdown of ...
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... MD pre-simulations of LJ argon are shown in Fig. 2b. A least-squares poly- nomial fit of 2nd order in density is also plotted: l ¼ 7:96 Â 10 À10 q 2 À 1:774 Â 10 À6 q þ 0:001106. This is then used in our enhanced CFD simulations to close the momentum equation. Again, for reference, data from the NIST database for liquid argon are also plotted in Fig. 2b. Note, due to the breakdown of the continuum assumption and the existence of non-local stress, this state-dependent viscosity becomes only approximate when applied to a nano-confined ...
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... substantially affect the bulk density measured. The no-slip CFD model does not exhibit large pressure drops at the inlet and the outlet due to the much lower velocity in the tube (and therefore, there are lower accelerations at the inlet and outlet) than in the slip cases. Cross-sectional velocity profiles in the centre of the CNT are plotted in Fig. 12a. The mass flow rate in the full MD simulation is measured to be 4:3 Â 10 À14 kg/s, which is 23 % greater than that predicted by our enhanced CFD. That this is a significant improvement on conventional CFD model pre- dictions is indicated in Table ...
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... the $ 2 nm diameter of the (15,15) CNT and despite the molecular layering that actually occurs within the flow field, as evidenced in Fig. 12b, our enhanced CFD approach can be considered reasonably robust in predicting important averaged fluid properties to the correct order of magnitude. These CFD results are obtained with negligible cost in comparison with full MD ...
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The usual boundary condition for liquids at macroscale is the no-slip condition. In micro and nanofluidic systems often liquid slippage at solid wall is observed. Nanoscale rough hydrophobic surfaces induce large liquid slippage due to entrapment of air pockets in the surface asperities (super-hydrophobic Cassie state). In this contribution we disc...
Citations
... When it comes to three-phase interfaces, processes such as evaporation [28,33,36,49] condensation [34,50,51], or solidification [52-54] on a surface also were widely investigated. Notably, MD methods can be also combined with the conventional Navier-Stokes approaches in the context of multi-scale modelling [55][56][57][58][59][60]. This integration of methodologies is very promising in addressing complex heat and mass trnasfer phenomena across different scales. ...
In the last decades, molecular dynamics (MD) simulations established as an important tool for solving fluid flow and heat transfer problems at the nanoscale, with a significant perspective impact on a wide range of industrial and scientific applications. As usual, this happened with several scholarly papers on this topic being published in the same period. The present article provides a thorough review of molecular dynamics (MD) simulations in the domain of fluid flow and heat transfer. In the first section, a survey of the physical modelling of heat transfer phenomena by MD simulations is presented, focusing on bubble and droplet nucleation and interfacial thermal behaviours. Subsequently, MD simulations of fluid flow and heat transfer in nanochannels are discussed, including adiabatic flow, convective heat transfer, and two-phase flow. Particular emphasis was placed on critical phenomena such as evaporation and condensation, to assess the effects of confinement within nanochannels. Finally, some of the current and emerging challenges in MD simulations and suggests future research directions are discussed.
... Quantification of slip in MD simulations is of great importance for the understanding of confined fluid systems, e.g., for multiscale simulations of fluid transport [70] or lubrication [22]. The characteristic transition from bulklike to wavelength-independent relaxation offers a new path to determine the slip length at equilibrium, as illustrated in Fig. 10. ...
Although continuum theories have been proven quite robust to describe confined fluid flow at molecular length scales, molecular dynamics (MD) simulations reveal mechanistic insights into the interfacial dissipation processes. Most MD simulations of confined fluids have used setups in which the lateral box size is not much larger than the gap height, thus breaking thin-film assumptions usually employed in continuum simulations. Here we explicitly probe the long-wavelength hydrodynamic correlations in confined simple fluids with MD and compare to gap-averaged continuum theories as typically applied in, e.g., lubrication. Relaxation times obtained from equilibrium fluctuations interpolate between the theoretical limits from bulk hydrodynamics and continuum formulations with increasing wavelength. We show how to exploit this characteristic transition to measure viscosity and slip length in confined systems simultaneously from equilibrium MD simulations. Moreover, the gap-averaged theory describes a geometry-induced dispersion relation that leads to overdamped sound relaxation at large wavelengths, which is confirmed by our MD simulations. Our results add to the understanding of transport processes under strong confinement and might be of technological relevance for the design of nanofluidic devices.
... In this research, the GROMACS software package (version 2020.6) (Holland, 2015) was used to perform all the molecular dynamics simulations and the following analysis. The simulations began with the creation of initial structures in which 15 of each molecule were randomly distributed in a box with 1 W% and suitable size. ...
... Quantification of slip in MD simulations is of great importance for the understanding of confined fluid systems, e. g. for multiscale simulations of fluid transport [71] or lubrication [23]. The characteristic transition from bulklike to wavelength-independent relaxation offers a new path to determine the slip length at equilibrium, as illustrated in Fig. 10. ...
Although continuum theories have been proven quite robust to describe confined fluid flow at molecular length scales, molecular dynamics (MD) simulations reveal mechanistic insights into the interfacial dissipation processes. Most MD simulations of confined fluids have used setups in which the lateral box size is not much larger than the gap height, thus breaking thin-film assumptions usually employed in continuum simulations. Here, we explicitly probe the long wavelength hydrodynamic correlations in confined simple fluids with MD and compare to gap-averaged continuum theories as typically applied in e.g. lubrication. Relaxation times obtained from equilibrium fluctuations interpolate between the theoretical limits from bulk hydrodynamics and continuum formulations with increasing wavelength. We show how to exploit this characteristic transition to measure viscosity and slip length in confined systems simultaneously from equilibrium MD simulations. Moreover, the gap-averaged theory describes a geometry-induced dispersion relation that leads to overdamped sound relaxation at large wavelengths, which is confirmed by our MD simulations. Our results add to the understanding of transport processes under strong confinement and might be of technological relevance for the design of nanofluidic devices due to the recent progress in fabrication methods.
... The molecular dynamics (MD) simulation was performed to investigate the stability and binding affinity between curcumin and modeled proteins (p53, Bax, and Bcl2). MD simulations were performed using the GROMACS (v2021.2) [39] software package. The initial structure for MD simulation was obtained from the docking process. ...
As the most common cancer in women, efforts have been made to develop novel nano-medicine-based therapeutics for breast cancer. In the present study, the in silico curcumin (Cur) properties were investigated, and we found some important drawbacks of Cur. To enhance cancer therapeutics of Cur, three different nonionic surfactants (span 20, 60, and 80) were used to prepare various Cur-loaded niosomes (Nio-Cur). Then, fabricated Nio-Cur were decorated with folic acid (FA) and polyethylene glycol (PEG) for breast cancer suppression. For PEG-FA@Nio-Cur, the gene expression levels of Bax and p53 were higher compared to free drug and Nio-Cur. With PEG-FA-decorated Nio-Cur, levels of Bcl2 were lower than the free drug and Nio-Cur. When MCF7 and 4T1 cell uptake tests of PEG-FA@Nio-Cur and Nio-Cur were investigated, the results showed that the PEG-FA-modified niosomes exhibited the most preponderant endocytosis. In vitro experiments demonstrate that PEG-FA@Nio-Cur is a promising strategy for the delivery of Cur in breast cancer therapy. Breast cancer cells absorbed the prepared nanoformulations and exhibited sustained drug release characteristics.
... One approach to improve the accuracy of continuum models is to perform hierarchical coupling to smaller scales [6]. For example, the viscosity [132,133] and slip length [134,135] have been calculated in NEMD simulations and then used as inputs in continuum models. ...
The prediction of friction under elastohydrodynamic lubrication (EHL) conditions remains one of the most important and controversial areas of tribology. This is mostly because the pressure and shear rate conditions inside EHL contacts are particularly severe, which complicates experimental design. Over the last decade, molecular dynamics (MD) simulation has played an increasingly significant role in our fundamental understanding of molecular behaviour under EHL conditions. In recent years, MD simulation has shown quantitative agreement with friction and viscosity results obtained experimentally, meaning that they can, either in isolation or through the use of multiscale coupling methods, begin to be used to test and inform macroscale models for EHL problems. This is particularly useful under conditions that are relevant inside machine components, but are difficult to obtain experimentally without uncontrollable shear heating.
... [2][3][4]8,18 However, this technique requires enormous computational resources when it is desired to study flow through pores longer and wider than a few tens of nanometers. 74 On the other hand, noncontinuum effects ranging from molecular ordering to velocity slip can inhibit the reliability of continuum fluid models such as CFD. 74 Is it possible to achieve more reliable and computationally efficient predictions toward gas transport in heterogeneous pore networks at a larger scale? ...
... 74 On the other hand, noncontinuum effects ranging from molecular ordering to velocity slip can inhibit the reliability of continuum fluid models such as CFD. 74 Is it possible to achieve more reliable and computationally efficient predictions toward gas transport in heterogeneous pore networks at a larger scale? The challenge lies in upscaling the simulation results achieved in a single pore, toward predicting flow transport through a pore matrix, as different phenomena involved in such multiscale porous matrices can affect the results. ...
Fluids confined in nanopores exhibit several unique structural and dynamical characteristics that affect a number of applications in industry as well as natural phenomena. Understanding and predicting the complex fluid behavior under nano-confinement is therefore of key importance, and both experimental and computational approaches have been employed toward this goal. It is now feasible to employ both simulations and theoretical methods, the results of which can be validated by cutting-edge experimental quantification. Nevertheless, predicting fluid transport through heterogeneous pore networks at a scale large enough to be relevant for practical applications remains elusive because one should account for a variety of fluid–rock interactions, a wide range of confined fluid states, as well as pore-edge effects and the existence of preferential pathways, which, together with many other phenomena, affect the results. The aim of this Review is to overview the significance of molecular phenomena on fluid transport in nanoporous media, the capability and shortcomings of both molecular and continuum fluid modeling approaches, and recent progress in multiscale modeling of fluid transport. In our interpretation, a multiscale approach couples a molecular picture for fluid interactions with solid surfaces at the single nanopore level with hierarchical transport analysis through realistic heterogeneous pore networks to balance physical accuracy with computational expense. When possible, comparison against experiments is provided as a guiding roadmap for selecting the appropriate computational methods. The appropriateness of an approach is certainly related to the final application of interest, as different sectors will require different levels of precision in the predictions.
... Holland et al. [198] employed MD pre-simulations for the simulations of flows in nanotubes. The dynamic viscosity and pressure are assumed to be polynomial functions of density. ...
Many heat transfer and fluid flow problems are multiscale in nature, and the multiscale numerical methods are needed to solve the problems by considering the phenomena in all the scales. In this paper, the current progresses of the multiscale simulations for fluid flow and heat transfer problems are reviewed. Brief introductions of the numerical methods in different scales are given, which include macroscopic continuum methods, mesoscopic particle-based lattice Boltzmann, direct simulation Monte Carlo, dissipative particle dynamics and microscopic molecular dynamics. Then the classifications, frameworks and general procedures of the multiscale methods are proposed and discussed. The multiscale methods are divided into the domain decomposition scheme and hierarchical scheme. For the domain decomposition, the information exchange techniques among the numerical methods in different scales are surveyed. Special attentions are paid to the characteristics of the mesoscopic methods that facilitate the coupling. The hierarchical scheme is further divided into serial, embedded and equation-free scheme based on the knowledge about macroscopic models. The corresponding multiscale methods are reviewed and compared. In addition, the coupling of time scales is discussed for the multiple-time-scale simulations. Finally, some issues and further developments about multiscale simulations are discussed, which include the terminology, spatial and temporal scale separation, the roles of mesoscopic methods and domain decomposition, the reduced-order models and the future applications.
... In this approach, the microscale part of the model is only loosely coupled with continuum fluid dynamics and run ahead of time to provide constitutive relations required for the macroscopic simulation, e.g. in the form of "look-up" tables. 17,18 However, this approach requires a significant scale separation between the microscopic and the macroscopic parts of the model for its validity. In comparison with the sequential models, the so-called concurrent models, where the interaction between all parts of the multiscale model is treated concurrently, are very challenging to develop to the state when they reach the same computationally efficiency. ...
A new implementation of the hybrid molecular dynamics – hydrodynamics methods based on the analogy with two-phase flows is developed that takes into account the feedback of molecular dynamics on hydrodynamics consistently. The consistency is achieved by deriving a discrete system of fluctuating hydrodynamic equations which solution converges to the locally averaged molecular dynamics field exactly in terms of the locally averaged fields. The new equations can be viewed as a generalisation of the classical continuum Landau-Lifshitz Fluctuating Hydrodynamics model in statistical mechanics to include a smooth transition from large-scale continuum hydrodynamics that obeys a Gaussian statistics to all-atom molecular dynamics. Similar to the classical Landau-Lifshitz Fluctuating Hydrodynamics model, the suggested Generalised Landau-Lifshitz Fluctuating Hydrodynamics equations are too complex for analytical solution, hence, a computational scheme for solving these equations is suggested. The scheme is implemented in a popular open-source molecular dynamics code GROMACS and numerical examples are provided for liquid argon simulations in equilibrium conditions and under macroscopic flow effects.
... An alternative, sequential, hybrid approach is to use lookup tables, whereby micro-simulations are performed ahead of time with the information stored in a table (Walter et al. 2013;Holland et al. 2015;Borg and Reese 2017). This table is then used as a surrogate model for all micro-simulations, with the macro-model interpolating between data entries whenever it requires micro-input. ...
We present a scheme for accelerating hybrid continuum-atomistic models in multiscale fluidic systems by using Gaussian process regression as a surrogate model for computationally expensive molecular dynamics simulations. Using Gaussian process regression, we are able to accurately predict atomic-scale information purely by consideration of the macroscopic continuum-model inputs and outputs and judge on the fly whether the uncertainty of our prediction is at an acceptable level, else a new molecular simulation is performed to continually augment the database, which is never required to be complete. This provides a substantial improvement over the current generation of hybrid methods, which often require many similar atomistic simulations to be performed, discarding information after it is used once. We apply our hybrid scheme to nano-confined unsteady flow through a high-aspect-ratio converging–diverging channel, and make comparisons between the new scheme and full molecular dynamics simulations for a range of uncertainty thresholds and initial databases. For low thresholds, our hybrid solution is highly accurate—around that of thermal noise. As the uncertainty threshold is raised, the accuracy of our scheme decreases and the computational speed-up increases (relative to a full molecular simulation), enabling the compromise between accuracy and efficiency to be tuned. The speed-up of our hybrid solution ranges from an order of magnitude, with no initial database, to cases where an extensive initial database ensures no new MD simulations are required.
